Adaptation of Maize to Temperate Climates: Mid-Density Genome-Wide Association Genetics and Diversity Patterns Reveal Key Genomic Regions, with a Major Contribution of the <i>Vgt2</i> (<i>ZCN8</i>) Locus

<div><p>The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives. Eighteen genomic regions were associated with flowering time. The number of early alleles cumulated along these regions was highly correlated with flowering time. Polymorphism in the vicinity of the <i>ZCN8</i> gene, which is the closest maize homologue to <i>Arabidopsis</i> major flowering time (<i>FT</i>) gene, had the strongest effect. This polymorphism is in the vicinity of the causal factor of <i>Vgt2</i> QTL. Diversity was lower, whereas differentiation and LD were higher for associated loci compared to the rest of the genome, which is consistent with selection acting on flowering time during maize migration. Selection tests also revealed supplementary loci that were highly differentiated among groups and not associated with flowering time in our panel, whereas they were in other linkage-based studies. This suggests that allele fixation led to a lack of statistical power when structure and relatedness were taken into account in a linear mixed model. Complementary designs and analysis methods are necessary to unravel the architecture of complex traits. Based on linkage disequilibrium (LD) estimates corrected for population structure, we concluded that the number of SNPs genotyped should be at least doubled to capture all QTLs contributing to the genetic architecture of polygenic traits in this panel. These results show that maize flowering time is controlled by numerous QTLs of small additive effect and that strong polygenic selection occurred under cool climatic conditions. They should contribute to more efficient genomic predictions of flowering time and facilitate the dissemination of diverse maize genetic resources under a wide range of environments.</p></div

Genome-wide linkage disequilibrium between all loci within and between chromosomes.

<p>The upper triangle corresponds to the LD <i>r²</i> measure calculated with Plink <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Purcell1" target="_blank">[50]</a>, the lower triangle to the LD r<i>²_s</i> measure <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Mangin1" target="_blank">[34]</a> corresponding to r<i>²</i> corrected for structure, using the Q matrix obtained with STRUCTURE software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Pritchard1" target="_blank">[40]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Falush1" target="_blank">[41]</a> and 55 SSRs. Values above 0.2 are highlighted by colored dots.</p

Diversity statistics computed using 29911 Panzea SNP markers over the whole panel and five main genetic groups.

a<p>Abb: abbreviation describing the group,</p>b<p>N_q = ∑_i δ_iq with i the index of lines and q the index of groups, δ_iq the assignment proportion of line i to group q according to STRUCTURE software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Pritchard1" target="_blank">[40]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Falush1" target="_blank">[41]</a> using 55 SSRs, Nq the number of lines in group q;</p>c<p>number of lines assigned to group q with a genome proportion above 0.8;</p>d<p>mean similarity within each group, calculated with IBS (identity by state);</p>e<p>expected heterozygosity inside each group computed with r-Hierfstat <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Goudet1" target="_blank">[46]</a>;</p><p>f percentage of polymorphic loci within each group,</p>d,e,f<p>statistics were computed considering lines with assignment to one group above 0.8.</p

Manhattan plot for female flowering (FFLW8) associations across the whole genome.

<p><i>P</i>-values were obtained with the mixed model including the structure matrix obtained using STRUCTURE software and 55 SSRs and the kinship matrix obtained with 94 SSRs and IBS measure. Horizontal dashed line indicates Bonferroni-corrected 5% significance threshold.</p

Distribution of SNP effects (GDD) according to the early allele frequency.

<p>In this figure, 673 markers with <i>P</i>-value<10⁻³ are represented. (A) For all inbred lines (rows) and SNPs (columns), red and blue colors correspond to the presence of late and early alleles, respectively. (B) The absolute SNP effect versus the frequency of the early allele for significant associations. Different colors correspond to different <i>P</i>-value thresholds.</p

Extent of linkage disequilibrium and number of markers needed to reach average <i>r²</i> = 0.1 for individual chromosomes and the whole genome.

<p>LD extent was computed with 43224 SNPs having MAF>0.05.</p>a<p>Physical distance to reach <i>r²</i> or <i>r²_s</i> equal to 0.1 estimated using the non-linear regression implemented in r-nls obtained by fitting Hill and Weir model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Hill1" target="_blank">[53]</a>. r<i>²</i> and <i>r²_s</i> obtained with Plink software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Purcell1" target="_blank">[50]</a> and r-LDcorSV <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071377#pone.0071377-Mangin1" target="_blank">[34]</a>, respectively. The number reported in brackets indicates the number of equidistant markers that would be needed to reach an average r<i>²</i> of 0.1 between adjacent markers;</p>b<p>number of markers used to estimate LD extent for each chromosome and the whole genome.</p